data

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v1.5.1 Latest Latest Go to latest Published: Mar 19, 2019 License: GPL-3.0 Imports: 11 Imported by: 1

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Repository

github.com/pbnjay/lollipops

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Documentation ¶

Index ¶

Constants
Variables
func GetProtID(symbol string) (string, error)
func GetProtMapping(dbname, geneid string) (string, error)
type GraphicFeature
type GraphicMetadata
type GraphicResponse

Constants ¶

View Source

const PfamGraphicURL = "http://pfam.xfam.org/protein/%s/graphic"

View Source

const UniprotDataURL = "https://www.uniprot.org/uniprot/%s.txt"

Variables ¶

View Source

var MotifNames = map[string]string{
	"disorder":       "Disordered region",
	"low_complexity": "Low complexity region",
	"sig_p":          "Signal peptide region",
	"coiled_coil":    "Coiled-coil motif",
	"transmembrane":  "Transmembrane region",
}

MotifNames has human-readable names

mostly from http://pfam.xfam.org/help#tabview=tab9

Functions ¶

func GetProtID ¶

func GetProtID(symbol string) (string, error)

func GetProtMapping ¶

func GetProtMapping(dbname, geneid string) (string, error)

Types ¶

type GraphicFeature ¶ added in v1.5.0

type GraphicFeature struct {
	Color    string          `json:"colour"`
	Text     string          `json:"text"`
	Type     string          `json:"type"`
	Start    json.Number     `json:"start"`
	End      json.Number     `json:"end"`
	Link     string          `json:"href"`
	Metadata GraphicMetadata `json:"metadata"`
}

GraphicFeature is a generic representation of various feature responses

type GraphicMetadata ¶ added in v1.5.0

type GraphicMetadata struct {
	Description string `json:"description"`
	Identifier  string `json:"identifier"`
}

type GraphicResponse ¶ added in v1.5.0

type GraphicResponse struct {
	Length   json.Number      `json:"length"`
	Metadata GraphicMetadata  `json:"metadata"`
	Motifs   []GraphicFeature `json:"motifs"`
	Regions  []GraphicFeature `json:"regions"`
}

func GetLocalGraphicData ¶ added in v1.5.0

func GetLocalGraphicData(filename string) (*GraphicResponse, error)

func GetPfamGraphicData ¶

func GetPfamGraphicData(accession string) (*GraphicResponse, error)

func GetUniprotGraphicData ¶ added in v1.5.0

func GetUniprotGraphicData(accession string) (*GraphicResponse, error)

Source Files ¶

View all Source files

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